City bus and subway boss Thomas Prendergast is being promoted to run the entire MTA, Gov. Cuomo announced yesterday in a move cheered by transit advocates.

Prendergast, president of NYC Transit since November 2009, headed the LIRR from 1991 to 1994. His new job will be a good cap to a 38-year transit career, said Robert Yaro, president of the Regional Plan Association.

“We have had four MTA directors in the last five years,” Yaro said. “We need a steady hand on the tiller.”

If confirmed by the state Senate, Prendergast will replace Joseph Lhota, who left the MTA on Jan. 1 to run for mayor.